3GT3

Structure of proteinase K with the mad triangle B3C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

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This is version 1.3 of the entry. See complete history


Literature

The magic triangle goes MAD: experimental phasing with a bromine derivative

Beck, T.Gruene, T.Sheldrick, G.M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 374-380

  • DOI: https://doi.org/10.1107/S0907444909051609
  • Primary Citation of Related Structures:  
    3GT3, 3GT4

  • PubMed Abstract: 

    Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br K edge was successfully carried out. Radiation damage to the bromine-carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out.


  • Organizational Affiliation

    Department of Structural Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany. tbeck@shelx.uni-ac.gwdg.de


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.84α = 90
b = 67.84β = 90
c = 101.77γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SADABSdata scaling
SHELXDphasing
SHELXL-97refinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-04-29
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description